Daylight Summer School 2001, June 5-7, Santa Fe, NM

Languages and Applications - Day 1
Lab/Lecture Outline and Links

Introduction

Languages

WhatNotesLinks
SMILES
  • Simple forms
  • SMILES syntax rules
  • Isomeric SMILES
  • Canonical SMILES
  • Reaction SMILES
SMARTS
  • Simple forms
  • SMARTS syntax rules
  • Atom and bond primitives, operators
  • Recursive SMARTS (vectors)
Reaction SMILES, SMARTS, and SMIRKS
  • SMILES are nomenclature
  • SMARTS are for matching/searching
  • SMIRKS are for transforming
Fingerprints
  • Fingerprints are bitmaps
  • Used for similarity and screening
Thor Data Trees (TDTs)
  • Datatypes
  • Root identifiers
  • Cross-reference identifiers
  • Non-identifiers (data)

Database Applications:

xvthor X Thor client
xvmerlin X Merlin client (and Thor client)
MCL Merlin Control Language
Thorfilters command-line Thor/Merlin tools
sthorman serial Thor/Merlin admin tool

Other Applications:

PrintPackage PostScript structure and data output
PCModels (ClogP and CMR) xvpcmodels, clogp and cmr apps
Clustering Package nearneighbors, jarpat, listclusters and showclusters
Rubicon Rule-based Invention of Conformers

Web Applications:

JavaGrins molecular and smarts editor applet and application
DayCGI web apps and tools
Other  

Documentation

Daylight Chemical Information Systems Inc.